Several next-generation DNA sequencing approaches, often referred to as “sequencing-by-synthesis” approaches, use repeated cycles of primer extension with a DNA polymerase to generate a sequence of signals containing nucleotide sequence information of populations of template molecules. See, e.g., Hert et al, ELECTROPHORESIS, 29:4618-4626 (2008); Metzker, NATURE REVIEWS GENETICS, 11:31-46 (2010); Droege et al, J. BIOTECHNOLOGY, 136:3-10 (2008). A common problem in these approaches is the “dephasing” of primer extensions because of the accumulation of the cycle-to-cycle effects of incomplete extension and/or inappropriate extensions (“carry forward”), which lead to significant reductions in the signal-to-noise ratio as sequencing progresses. See, e.g., Ronaghi, GENOME RESEARCH, 11:3-11 (2001); Leamon et al, CHEMICAL REVIEWS, 107:3367-3376 (2007); Chen et al, International Patent Publication WO 2007/098049. Currently, such inefficiencies are dealt with by signal processing software, such as those described in Leamon et al. (cited above) and Chen et al. (cited above). But as longer read lengths and alternative detection schemes are sought, such as schemes for label-free extension detection (see, e.g., Rothberg et al, U.S. Patent Publication 2009/0127589), alternative methods for addressing signal loss from incomplete extension or carry forward errors would be highly desirable.